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@ -11,145 +11,154 @@ http://stackoverflow.com/users/4290753/once
##Handy Bash 'oneliner' commands for tsv file editing ##Handy Bash 'oneliner' commands for tsv file editing
- Grep
- Sed
- Awk
- Xargs
- Find
- Others
##Grep ##Grep
extract text bewteen words (e.g. w1,w2) extract text bewteen words (e.g. w1,w2)
grep -o -P '(?<=w1).*(?=w2)' grep -o -P '(?<=w1).*(?=w2)'
>grep lines without word (e.g. bbo) >grep lines without word (e.g. bbo)
$ grep -v bbo grep -v bbo
>grep and count (e.g. bbo) >grep and count (e.g. bbo)
$grep -c bbo filename grep -c bbo filename
>insensitive grep (e.g. bbo/BBO/Bbo) >insensitive grep (e.g. bbo/BBO/Bbo)
$grep -i "bbo" filename grep -i "bbo" filename
>count occurrence (e.g. three times a line count three times) >count occurrence (e.g. three times a line count three times)
$grep -o bbo filename grep -o bbo filename
>COLOR the match (e.g. bbo)! >COLOR the match (e.g. bbo)!
$grep --color bbo filename grep --color bbo filename
>grep search all files in a directory(e.g. bbo) >grep search all files in a directory(e.g. bbo)
$grep -R bbo /path/to/directory or grep -R bbo /path/to/directory or
$grep -r bbo /path/to/directory grep -r bbo /path/to/directory
>search all files in directory, only output file names with matches(e.g. bbo) >search all files in directory, only output file names with matches(e.g. bbo)
$grep -Rh bbo /path/to/directory or grep -Rh bbo /path/to/directory or
$grep -rh bbo /path/to/directory grep -rh bbo /path/to/directory
>grep OR (e.g. A or B or C or D) >grep OR (e.g. A or B or C or D)
$grep 'A\|B\|C\|D' grep 'A\|B\|C\|D'
>grep AND (e.g. A and B) >grep AND (e.g. A and B)
$grep 'A.*B' grep 'A.*B'
>grep all content of a fileA from fileB >grep all content of a fileA from fileB
$grep -f fileA fileB grep -f fileA fileB
>grep a tab >grep a tab
$grep $'\t' grep '\t'
>>Sed #Sed
>remove lines with word (e.g. bbo) >remove lines with word (e.g. bbo)
$sed "/bbo/d" filename sed "/bbo/d" filename
>edit infile (edit and save) >edit infile (edit and save)
$sed -i "/bbo/d" filename sed -i "/bbo/d" filename
>when using variable (e.g. $i), use double quotes " " >when using variable (e.g. i), use double quotes " "
e.g. add >$i to the first line (to make a FASTA file) e.g. add > i to the first line (to make a FASTA file)
$sed "1i >$i" sed "1i > i"
//notice the double quotes! in other examples, you can use a single quote, but here, no way! //notice the double quotes! in other examples, you can use a single quote, but here, no way!
//'1i' means insert to first line //'1i' means insert to first line
>delete empty lines >delete empty lines
$sed '/^\s*$/d' or sed '/^\s* /d' or
$sed 's/^$/d' sed 's/^ /d'
>delete last line >delete last line
$sed '$d' sed ' d'
>add \n every nth character (e.g. every 4th character) >add \n every nth character (e.g. every 4th character)
$sed 's/.\{4\}/&\n/g' sed 's/.\{4\}/&\n/g'
>substitution (e.g. replace A by B) >substitution (e.g. replace A by B)
$sed 's/A/B/g' filename sed 's/A/B/g' filename
>select lines start with string (e.g. bbo) >select lines start with string (e.g. bbo)
$sed -n '/^@S/p' sed -n '/^@S/p'
>delete lines with string (e.g. bbo) >delete lines with string (e.g. bbo)
$sed '/bbo/d' filename sed '/bbo/d' filename
>print every nth lines >print every nth lines
$sed -n '0~3p' filename sed -n '0~3p' filename
//catch 0: start; 3: step //catch 0: start; 3: step
>print every odd # lines >print every odd # lines
$sed -n '1~2p' sed -n '1~2p'
>print every third line including the first line >print every third line including the first line
$sed -n '1p;0~3p' sed -n '1p;0~3p'
>remove leading whitespace and tabs >remove leading whitespace and tabs
$sed -e 's/^[ \t]*//' sed -e 's/^[ \t]*//'
//notice a whitespace before '\t'!! //notice a whitespace before '\t'!!
>remove only leading whitespace >remove only leading whitespace
$sed 's/ *//' sed 's/ *//'
//notice a whitespace before '*'!! //notice a whitespace before '*'!!
>remove ending commas >remove ending commas
$sed 's/,$//g' sed 's/, //g'
>add a column to the end >add a column to the end
$sed "s/$/\t$i/" sed "s/ /\t i/"
//$i is the valuable you want to add // i is the valuable you want to add
e.g. add the filename to every last column of the file e.g. add the filename to every last column of the file
$for i in $(ls);do sed -i "s/$/\t$i/" $i;done for i in (ls);do sed -i "s/ /\t i/" i;done
>remove newline\ nextline >remove newline\ nextline
$sed ':a;N;$!ba;s/\n//g' sed ':a;N; !ba;s/\n//g'
>>Awk #Awk
>set tab as field separator >set tab as field separator
$awk -F $'\t' awk -F '\t'
>output as tab separated (also as field separator) >output as tab separated (also as field separator)
$awk -v OFS='\t' awk -v OFS='\t'
>pass variable >pass variable
a=bbo;b=obb; a=bbo;b=obb;
awk -v a="$a" -v b="$b" "$1==a && $10=b' filename awk -v a=" a" -v b=" b" " 1==a && 10=b' filename
>print number of characters on each line >print number of characters on each line
$awk '{print length ($0);}' filename awk '{print length ( 0);}' filename
>find number of columns >find number of columns
$awk '{print NF}' awk '{print NF}'
>reverse column order >reverse column order
$awk '{print $2, $1}' awk '{print 2, 1}'
>check if there is a comma in a column (e.g. column $1) >check if there is a comma in a column (e.g. column 1)
$awk '$1~/,/ {print}' awk ' 1~/,/ {print}'
>split and do for loop >split and do for loop
$awk '{split($2, a,",");for (i in a) print $1"\t"a[i]} filename awk '{split( 2, a,",");for (i in a) print 1"\t"a[i]} filename
>print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times) >print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times)
$awk -v N=7 '{print}/bbo/&& --N<=0 {exit}' awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'
>add string to the beginning of a column (e.g add "chr" to column $3) >add string to the beginning of a column (e.g add "chr" to column 3)
$awk 'BEGIN{OFS="\t"}$3="chr"$3' awk 'BEGIN{OFS="\t"} 3="chr" 3'
>remove lines with string (e.g. bbo) >remove lines with string (e.g. bbo)
$awk '!/bbo/' file awk '!/bbo/' file
>column subtraction >column subtraction
$cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}' cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+= 3- 2}END{print SUM}'
>usage and meaning of NR and FNR >usage and meaning of NR and FNR
e.g. e.g.
@ -160,7 +169,7 @@ c
fileB: fileB:
d d
e e
$awk 'print FILENAME, NR,FNR,$0}' fileA fileB fileA 1 1 a awk 'print FILENAME, NR,FNR, 0}' fileA fileB fileA 1 1 a
fileA 2 2 b fileA 2 2 b
fileA 3 3 c fileA 3 3 c
fileB 4 1 d fileB 4 1 d
@ -178,281 +187,281 @@ fileB:
2 1 2 1
3 0 3 0
4 1 4 1
$awk -v OFS='\t' 'NR=FNR{a[$1]=$2;next} NF {print $1,((a[$1]=$2)? $2:"0")}' fileA fileB 1 0 awk -v OFS='\t' 'NR=FNR{a[ 1]= 2;next} NF {print 1,((a[ 1]= 2)? 2:"0")}' fileA fileB 1 0
2 1 2 1
3 0 3 0
4 0 4 0
>round all numbers of file (e.g. 2 significant figure) >round all numbers of file (e.g. 2 significant figure)
$awk '{while (match($0, /[0-9]+\[0-9]+/)){ awk '{while (match( 0, /[0-9]+\[0-9]+/)){
\printf "%s%.2f", substr($0,0,RSTART-1),substr($0,RSTART,RLENGTH) \printf "%s%.2f", substr( 0,0,RSTART-1),substr( 0,RSTART,RLENGTH)
\$0=substr($0, RSTART+RLENGTH) \ 0=substr( 0, RSTART+RLENGTH)
\} \}
\print \print
\}' \}'
>give number/index to every row >give number/index to every row
$awk '{printf("%s\t%s\n",NR,$0)}' awk '{printf("%s\t%s\n",NR, 0)}'
>>Xargs #Xargs
>set tab as delimiter (default:space) >set tab as delimiter (default:space)
$xargs -d\t xargs -d\t
>display 3 items per line >display 3 items per line
$echo 1 2 3 4 5 6| xargs -n 3 echo 1 2 3 4 5 6| xargs -n 3
//1 2 3 //1 2 3
4 5 6 4 5 6
>prompt before execution >prompt before execution
$echo a b c |xargs -p -n 3 echo a b c |xargs -p -n 3
>print command along with output >print command along with output
$xargs -t abcd xargs -t abcd
///bin/echo abcd ///bin/echo abcd
//abcd //abcd
>with find and rm >with find and rm
$find . -name "*.html"|xargs rm -rf find . -name "*.html"|xargs rm -rf
>delete fiels with whitespace in filename (e.g. "hello 2001") >delete fiels with whitespace in filename (e.g. "hello 2001")
$find . -name "*.c" -print0|xargs -0 rm -rf find . -name "*.c" -print0|xargs -0 rm -rf
>show limits >show limits
$xargs --show-limits xargs --show-limits
>move files to folder >move files to folder
$find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old
or or
$find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old
>move first 100th files to a directory (e.g. d1) >move first 100th files to a directory (e.g. d1)
$ls |head -100|xargs -I {} mv {} d1 ls |head -100|xargs -I {} mv {} d1
>parallel >parallel
$time echo {1..5} |xargs -n 1 -P 5 sleepa lot faster than time echo {1..5} |xargs -n 1 -P 5 sleepa lot faster than
$time echo {1..5} |xargs -n1 sleep time echo {1..5} |xargs -n1 sleep
>copy all files from A to B >copy all files from A to B
$find /dir/to/A -type f -name "*.py" -print 0| xargs -0 -r -I file cp -v -p file --target-directory=/path/to/B find /dir/to/A -type f -name "*.py" -print 0| xargs -0 -r -I file cp -v -p file --target-directory=/path/to/B
//v: verbose| //v: verbose|
//p: keep detail (e.g. owner) //p: keep detail (e.g. owner)
>with sed >with sed
$ls |xargs -n1 -I file sed -i '/^Pos/d' filename ls |xargs -n1 -I file sed -i '/^Pos/d' filename
>add the file name to the first line of file >add the file name to the first line of file
$ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt
>count all files >count all files
$ls |xargs -n1 wc -l ls |xargs -n1 wc -l
>to filter txt to a single line >to filter txt to a single line
$ls -l| xargs ls -l| xargs
>count files within directories >count files within directories
$echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' -- echo mso{1..8}|xargs -n1 bash -c 'echo -n " 1:"; ls -la " 1"| grep -w 74 |wc -l' --
// "--" signals the end of options and display further option processing // "--" signals the end of options and display further option processing
>download dependencies files and install (e.g. requirements.txt) >download dependencies files and install (e.g. requirements.txt)
$cat requirements.txt| xargs -n1 sudo pip install cat requirements.txt| xargs -n1 sudo pip install
>count lines in all file, also count total lines >count lines in all file, also count total lines
$ls|xargs wc -l ls|xargs wc -l
>>Find #Find
>list all sub directory/file in the current directory >list all sub directory/file in the current directory
$find . find .
>list all files under the current directory >list all files under the current directory
$find . -type f find . -type f
>list all directories under the current directory >list all directories under the current directory
$find . -type d find . -type d
>edit all files under current directory (e.g. replace 'www' with 'ww') >edit all files under current directory (e.g. replace 'www' with 'ww')
$find . name '*.php' -exec sed -i 's/www/w/g' {} \; find . name '*.php' -exec sed -i 's/www/w/g' {} \;
>if no subdirectory >if no subdirectory
$replace "www" "w" -- * replace "www" "w" -- *
//a space before * //a space before *
>find and output only filename (e.g. "mso") >find and output only filename (e.g. "mso")
$find mso*/ -name M* -printf "%f\n" find mso*/ -name M* -printf "%f\n"
>find and delete file with size less than (e.g. 74 byte) >find and delete file with size less than (e.g. 74 byte)
$find . -name "*.mso" -size -74c -delete find . -name "*.mso" -size -74c -delete
//M for MB, etc //M for MB, etc
>>Others #Others
>remove newline / nextline >remove newline / nextline
$tr --delete '\n' <input.txt >output.txt tr --delete '\n' <input.txt >output.txt
>replace newline >replace newline
$ tr '\n' ' ' <filename tr '\n' ' ' <filename
>compare files (e.g. fileA, fileB) >compare files (e.g. fileA, fileB)
$diff fileA fileB diff fileA fileB
//a: added; d:delete; c:changed //a: added; d:delete; c:changed
or or
$sdiff fileA fileB sdiff fileA fileB
//side-to-side merge of file differences //side-to-side merge of file differences
>number a file (e.g. fileA) >number a file (e.g. fileA)
$nl fileA nl fileA
or or
$nl -nrz fileA nl -nrz fileA
//add leading zeros //add leading zeros
>combine/ paste two files (e.g. fileA, fileB) >combine/ paste two files (e.g. fileA, fileB)
$paste fileA fileB paste fileA fileB
//default tab seperated //default tab seperated
>reverse string >reverse string
$echo 12345| rev echo 12345| rev
>read .gz file without extracting >read .gz file without extracting
$zmore filename zmore filename
or or
$zless filename zless filename
>run in background, output error file >run in background, output error file
$(command here) 2>log & (command here) 2>log &
or or
$(command here) 2>&1| tee logfile (command here) 2>&1| tee logfile
or or
$(command here) 2>&1 >>outfile (command here) 2>&1 >>outfile
//0: standard input; 1: standard output; 2: standard error //0: standard input; 1: standard output; 2: standard error
>send mail >send mail
$echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com
//use -a flag to set send from (-a "From: some@mail.tld") //use -a flag to set send from (-a "From: some@mail.tld")
>.xls to csv >.xls to csv
$xls2csv filename xls2csv filename
>append to file (e.g. hihi) >append to file (e.g. hihi)
$echo 'hihi' >>filename echo 'hihi' >>filename
>make BEEP found >make BEEP found
$speaker-test -t sine -f 1000 -l1 speaker-test -t sine -f 1000 -l1
>set beep duration >set beep duration
$(speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid (speaker-test -t sine -f 1000) & pid= !;sleep 0.1s;kill -9 pid
>history edit/ delete >history edit/ delete
$~/.bash_history ~/.bash_history
or or
$history -d [line_number] history -d [line_number]
>get last history/record filename >get last history/record filename
$head !$ head !
>clean screen >clean screen
$clear clear
or or
$Ctrl+l Ctrl+l
>send data to last edited file >send data to last edited file
$cat /directory/to/file cat /directory/to/file
$echo 100>!$ echo 100>!
>run history number (e.g. 53) >run history number (e.g. 53)
$!53 !53
>run last command >run last command
$!! !!
>run last command that began with (e.g. cat filename) >run last command that began with (e.g. cat filename)
$!cat !cat
or or
$!c !c
//run cat filename again //run cat filename again
>extract .xf >extract .xf
1. $unxz filename.tar.xz 1. unxz filename.tar.xz
2. $tar -xf filename.tar 2. tar -xf filename.tar
>install python package >install python package
$pip install packagename pip install packagename
>random order (lucky draw) >random order (lucky draw)
$for i in a b c d e; do echo $i; done| shuf for i in a b c d e; do echo i; done| shuf
>echo a random number >echo a random number
$echo $RANDOM echo RANDOM
>Download file if necessary >Download file if necessary
$data=file.txt data=file.txt
url=http://www.example.com/$data url=http://www.example.com/ data
if [! -s $data];then if [! -s data];then
echo "downloading test data..." echo "downloading test data..."
wget $url wget url
fi fi
>wget to a filename (when a long name) >wget to a filename (when a long name)
$wget -O filename "http://example.com" wget -O filename "http://example.com"
>wget files to a folder >wget files to a folder
$wget -P /path/to/directory "http://example.com" wget -P /path/to/directory "http://example.com"
>delete current bash command >delete current bash command
$Ctrl+U Ctrl+U
or or
$Ctrl+C Ctrl+C
or or
$Alt+Shift+# Alt+Shift+#
//to make it to history //to make it to history
>add things to history (e.g. "addmetohistory") >add things to history (e.g. "addmetohistory")
$#addmetodistory #addmetodistory
//just add a "#" before~~ //just add a "#" before~~
>sleep awhile or wait for a moment or schedule a job >sleep awhile or wait for a moment or schedule a job
$sleep 5;echo hi sleep 5;echo hi
>count the time for executing a command >count the time for executing a command
$time echo hi time echo hi
>backup with rsync >backup with rsync
$rsync -av filename filename.bak rsync -av filename filename.bak
$rsync -av directory directory.bak rsync -av directory directory.bak
$rsync -av --ignore_existing directory/ directory.bak rsync -av --ignore_existing directory/ directory.bak
$rsync -av --update directory directory.bak rsync -av --update directory directory.bak
//skip files that are newer on receiver (i prefer this one!) //skip files that are newer on receiver (i prefer this one!)
>make all directories at one time! >make all directories at one time!
$mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat} mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat}
//-p: make parent directory //-p: make parent directory
//this will create project/doc/html/; project/doc/info; project/lib/ext ,etc //this will create project/doc/html/; project/doc/info; project/lib/ext ,etc
>run command only if another command returns zero exit status (well done) >run command only if another command returns zero exit status (well done)
$cd tmp/ && tar xvf ~/a.tar cd tmp/ && tar xvf ~/a.tar
>run command only if another command returns non-zero exit status (not finish) >run command only if another command returns non-zero exit status (not finish)
$cd tmp/a/b/c ||mkdir -p tmp/a/b/c cd tmp/a/b/c ||mkdir -p tmp/a/b/c
>extract to a path >extract to a path
$tar xvf -C /path/to/directory filename.gz tar xvf -C /path/to/directory filename.gz
>use backslash "\" to break long command >use backslash "\" to break long command
$cd tmp/a/b/c \ cd tmp/a/b/c \
> || \ > || \
>mkdir -p tmp/a/b/c >mkdir -p tmp/a/b/c
>get pwd >get pwd
$VAR=$PWD; cd ~; tar xvf -C $VAR file.tar VAR= PWD; cd ~; tar xvf -C VAR file.tar
//PWD need to be capital letter //PWD need to be capital letter
>list file type of file (e.g. /tmp/) >list file type of file (e.g. /tmp/)
$file /tmp/ file /tmp/
//tmp/: directory //tmp/: directory
>bash script >bash script
#!/bin/bash #!/bin/bash
file=${1#*.} file= {1#*.}
//remove string before a "." //remove string before a "."
file=${1%.*} file= {1%.*}
//remove string after a "." //remove string after a "."